Package: ALL Version: 1.4.1 Depends: Biobase (>= 1.12.0) Title: A data package Description: Data of T- and B-cell Acute Lymphocytic Leukemia from the Ritz Laboratory at the DFCI (includes Apr 2004 versions) biocViews: ExperimentData Author: Xiaochun Li Maintainer: Xiaochun Li License: GPL source.ver: src/contrib/ALL_1.4.1.tar.gz win.binary.ver: bin/windows/contrib/2.4/ALL_1.4.1.zip mac.binary.ver: bin/macosx/universal/contrib/2.4/ALL_1.4.1.tgz vignettes: vignettes/ALL/inst/doc/ALLintro-003.pdf, vignettes/ALL/inst/doc/ALLintro.pdf Package: ALLMLL Version: 1.2.0 Depends: R (>= 2.4.0), affy Title: A subset of arrays from a large acute lymphoblastic leukemia (ALL) study Description: This package provides probe-level data for 20 HGU133A and 20 HGU133B arrays which are a subset of arrays from a large ALL study. The data is for the MLL arrays. This data was published in Mary E. Ross, Xiaodong Zhou, Guangchun Song, Sheila A. Shurtleff, Kevin Girtman, W. Kent Williams, Hsi-Che Liu, Rami Mahfouz, Susana C. Raimondi, Noel Lenny, Anami Patel, and James R. Downing (2003) Classification of pediatric acute lymphoblastic leukemia by gene expression profiling Blood 102: 2951-2959 biocViews: ExperimentData Author: B. M. Bolstad License: GPL version 2.0 source.ver: src/contrib/ALLMLL_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.4/ALLMLL_1.2.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.4/ALLMLL_1.2.0.tgz Package: AmpAffyExample Version: 1.2.0 Depends: R (>= 2.4.0), affy (>= 1.2) Suggests: hgu133acdf Title: Example of Amplified Data Description: Six arrays. Three from amplified RNA, three from the typical procedure. biocViews: ExperimentData Author: Rafael A. Irizarry Maintainer: Rafael A. Irizarry License: LGPL version 2 or newer source.ver: src/contrib/AmpAffyExample_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.4/AmpAffyExample_1.2.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.4/AmpAffyExample_1.2.0.tgz Package: beta7 Version: 0.6.0 Depends: R (>= 2.4.0), marray Title: Rodriguez et al. (2004) Differential Gene Expression by Memory/Effector T Helper Cells Bearing the Gut-Homing Receptor Integrin alpha4 beta7. Description: Data from 6 gpr files aims to identify differential expressed genes between the beta 7+ and beta 7- memory T helper cells. biocViews: ExperimentData Author: Jean Yang Maintainer: Jean Yang License: LGPL source.ver: src/contrib/beta7_0.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.4/beta7_0.6.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.4/beta7_0.6.0.tgz Package: bronchialIL13 Version: 1.0-0 Depends: affy Title: time course experiment involving il13 Description: derived from CNMC (pepr.cnmcresearch.org) http://pepr.cnmcresearch.org/browse.do?action=list_prj_exp&projectId=95 Human Bronchial Cell line A549 Author: Vince Carey Maintainer: Vince Carey URL: http://www.biostat.harvard.edu/~carey License: GPL2 source.ver: src/contrib/bronchialIL13_1.0-0.tar.gz win.binary.ver: bin/windows/contrib/2.4/bronchialIL13_1.0-0.zip mac.binary.ver: bin/macosx/universal/contrib/2.4/bronchialIL13_1.0-0.tgz Package: CLL Version: 1.2.2 Depends: R (>= 2.4.0), affy (>= 1.13.10), Biobase (>= 1.13.23) Title: A Package for CLL Gene Expression Data Description: The CLL package contains the chronic lymphocytic leukemia (CLL) gene expression data. The CLL data had 24 samples that were either classified as progressive or stable in regards to disease progression. The data came from Dr. Sabina Chiaretti at Division of Hematology, Department of Cellular Biotechnologies and Hematology, University La Sapienza, Rome, Italy and Dr. Jerome Ritz at Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts. biocViews: ExperimentData Author: Elizabeth Whalen Maintainer: Elizabeth Whalen License: LGPL source.ver: src/contrib/CLL_1.2.2.tar.gz win.binary.ver: bin/windows/contrib/2.4/CLL_1.2.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.4/CLL_1.2.1.tgz Package: colonCA Version: 1.4.0 Depends: Biobase (>= 1.11.12) Title: exprSet for Alon et al. (1999) colon cancer data Description: exprSet for Alon et al. (1999) colon cancer data biocViews: ExperimentData Author: Sylvia Merk Maintainer: W Sylvia Merk License: unknown source.ver: src/contrib/colonCA_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.4/colonCA_1.4.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.4/colonCA_1.4.0.tgz Package: davidTiling Version: 1.2.1 Depends: R (>= 2.3.0), Biobase (>= 1.12.0), tilingArray (>= 1.8.22), GO Title: Data and analysis scripts for David, Huber et al. yeast tiling array paper Description: This package contains the data for the paper cited below: 8 CEL files of Affymetrix genechips, the eSet object, a probe annotation data structure for the chip, and the yeast genome annotation (GFF file) that was used. In addition, some custom-written analysis functions are provided, as well as R scripts in the scripts directory. Author: Wolfgang Huber , Joern Toedling Maintainer: Wolfgang Huber URL: http://www.ebi.ac.uk/huber License: LGPL source.ver: src/contrib/davidTiling_1.2.1.tar.gz win.binary.ver: bin/windows/contrib/2.4/davidTiling_1.2.1.zip mac.binary.ver: bin/macosx/universal/contrib/2.4/davidTiling_1.2.1.tgz Package: ecoliLeucine Version: 1.2.0 Depends: R (>= 1.9.0), affy Title: Experimental data with Affymetrix E. coli chips Description: Experimental data with Affymetrix E. coli chips, as reported in She-pin Hung, Pierre Baldi, and G. Wesley Hatfield, J. Biol. Chem., Vol. 277, Issue 43, 40309-40323, October 25, 2002 biocViews: ExperimentData Author: Laurent Gautier Maintainer: Laurent License: GPL version 2 or newer source.ver: src/contrib/ecoliLeucine_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.4/ecoliLeucine_1.2.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.4/ecoliLeucine_1.2.0.tgz Package: estrogen Version: 1.8.0 Depends: R (>= 1.9.0), affy (>= 1.4) Title: 2x2 factorial design exercise for the Bioconductor short course Description: Data from 8 Affymetrix genechips, looking at a 2x2 factorial design (with 2 repeats per level) Author: Wolfgang Huber, Robert Gentleman Maintainer: R. Gentleman License: LGPL source.ver: src/contrib/estrogen_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.4/estrogen_1.8.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.4/estrogen_1.8.0.tgz vignettes: vignettes/estrogen/inst/doc/estrogen-boxplotb.pdf, vignettes/estrogen/inst/doc/estrogen-hist.pdf, vignettes/estrogen/inst/doc/estrogen.pdf Package: faahKO Version: 1.2.0 Depends: R Suggests: xcms Title: Saghatelian et al. (2004) FAAH knockout LC/MS data Description: Positive ionization mode data in NetCDF file format. Centroided subset from 200-600 m/z and 2500-4500 seconds. Data originally reported in "Assignement of Endogenous Substrates to Enzymes by Global Metabolite Profiling" Biochemistry; 2004; 43(45). Also includes detected peaks in an xcmsSet. Author: Colin A. Smith Maintainer: Colin A. Smith URL: http://dx.doi.org/10.1021/bi0480335 License: unknown source.ver: src/contrib/faahKO_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.4/faahKO_1.2.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.4/faahKO_1.2.0.tgz Package: facsDorit Version: 1.4.0 Depends: R (>= 1.9.1), prada (>= 1.0.5) Title: DKFZ FACS example data Description: FACS example data for cell-based assays. This data is used in the examples and vignettes of the package prada. biocViews: ExperimentData Author: Florian Hahne Maintainer: Florian Hahne URL: http://www.dkfz.de/mga License: GPL2 source.ver: src/contrib/facsDorit_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.4/facsDorit_1.4.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.4/facsDorit_1.4.0.tgz Package: fibroEset Version: 1.4.1 Depends: Biobase (>= 1.12.0) Title: exprSet for Karaman et al. (2003) fibroblasts data Description: exprSet for Karaman et al. (2003) human, bonobo and gorilla fibroblasts data biocViews: ExperimentData Author: Sylvia Merk Maintainer: Sylvia Merk License: unknown source.ver: src/contrib/fibroEset_1.4.1.tar.gz win.binary.ver: bin/windows/contrib/2.4/fibroEset_1.4.1.zip mac.binary.ver: bin/macosx/universal/contrib/2.4/fibroEset_1.4.1.tgz Package: gaschYHS Version: 1.0.0 Depends: Biobase (>= 1.12.0) Title: ExpressionSet for response of yeast to heat shock and other environmental stresses Description: Data from PMID 11102521 biocViews: ExperimentData Author: Audrey Gasch and colleagues Maintainer: Vince Carey License: unknown, repackages data on http://genome-www.stanford.edu/yeast_stress/data/ rawdata/complete_dataset.txt source.ver: src/contrib/gaschYHS_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.4/gaschYHS_1.0.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.4/gaschYHS_1.0.0.tgz Package: GGdata Version: 0.0-6 Depends: R (>= 2.4.0), Biobase (>= 1.11.41), hgfocus Title: software and data for genetical genomics Description: data exemplars dealing with hapmap SNP reports, GWAS, etc. Author: stvjc Maintainer: stvjc License: LGPL source.ver: src/contrib/GGdata_0.0-6.tar.gz mac.binary.ver: bin/macosx/universal/contrib/2.4/GGdata_0.0-5.tgz Package: golubEsets Version: 1.4.2 Depends: Biobase (>= 1.12.0) Title: exprSets for golub leukemia data Description: representation of public golub data with some covariate data of provenance unknown to the maintainer at present; now employs ExpressionSet format biocViews: ExperimentData Author: Todd Golub Maintainer: Vince Carey License: unknown source.ver: src/contrib/golubEsets_1.4.2.tar.gz win.binary.ver: bin/windows/contrib/2.4/golubEsets_1.4.2.zip mac.binary.ver: bin/macosx/universal/contrib/2.4/golubEsets_1.4.2.tgz Package: harbChIP Version: 0.0.1 Depends: Biobase Title: Experimental Data Package: harbChIP Description: Data Package automatically created on Fri Dec 1 09:47:22 2006. biocViews: ExperimentData Author: VJ Carey Maintainer: VJ Carey, License: The Artistic License, Version 2.0 source.ver: src/contrib/harbChIP_0.0.1.tar.gz Package: HEEBOdata Version: 1.0.0 Title: HEEBO set and HEEBO controls. Description: R objects describing the HEEBO oligo set. biocViews: ExperimentData Author: Agnes Paquet Maintainer: Agnes Paquet URL: http://alizadehlab.stanford.edu/ http://arrays.ucsf.edu/ License: LGPL source.ver: src/contrib/HEEBOdata_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.4/HEEBOdata_1.0.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.4/HEEBOdata_1.0.0.tgz Package: hgu2beta7 Version: 1.2.0 Depends: R(>= 2.0.0) Title: A data package containing annotation data for hgu2beta7 Description: Annotation data file for hgu2beta7 assembled using data from public data repositories biocViews: AnnotationData Author: Lin, Chenwei Maintainer: Ting-Yuan Liu License: LGPL source.ver: src/contrib/hgu2beta7_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.4/hgu2beta7_1.2.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.4/hgu2beta7_1.2.0.tgz Package: HIVcDNAvantWout03 Version: 1.2.0 Title: T cell line infections with HIV-1 LAI (BRU) Description: {The expression levels of approximately 4600 cellular RNA transcripts were assessed in CD4+ T cell lines at different times after infection with HIV-1BRU using DNA microarrays. This data corresponds to the first block of a 12 block array image (001030_08_1.GEL) in the first data set (2000095918 A) in the first experiment (CEM LAI vs HI-LAI 24hr). There are two data sets, which are part of a dye-swap experiment with replicates, representing the Cy3 (green) absorption intensities for channel 1 (hiv1raw) and the Cy5 (red) absorption intensities for channel 2 (hiv2raw). } Author: Dr. Angelique van't Wout, Department of Microbiology, University of Washington Maintainer: Chris Fraley URL: http://expression.microslu.washington.edu/expression/vantwoutjvi2002.html License: GPL version 2 or higher source.ver: src/contrib/HIVcDNAvantWout03_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.4/HIVcDNAvantWout03_1.2.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.4/HIVcDNAvantWout03_1.2.0.tgz vignettes: vignettes/HIVcDNAvantWout03/inst/doc/hivData.pdf Package: Iyer517 Version: 1.4.1 Depends: Biobase (>= 1.12.0) Title: exprSets for Iyer, Eisen et all 1999 Science paper Description: representation of public Iyer data from http://genome-www.stanford.edu/serum/clusters.html biocViews: ExperimentData Author: Vishy Iyer Maintainer: Vince Carey License: unknown source.ver: src/contrib/Iyer517_1.4.1.tar.gz win.binary.ver: bin/windows/contrib/2.4/Iyer517_1.4.1.zip mac.binary.ver: bin/macosx/universal/contrib/2.4/Iyer517_1.4.1.tgz vignettes: vignettes/Iyer517/inst/doc/Iyer517.pdf Package: kidpack Version: 1.4.1 Depends: R (>= 2.4.0), Biobase (>= 1.12.0) Title: DKFZ kidney package Description: kidney microarray data biocViews: ExperimentData Author: Wolfgang Huber Maintainer: Wolfgang Huber URL: http://www.dkfz.de/mga License: GPL2 source.ver: src/contrib/kidpack_1.4.1.tar.gz win.binary.ver: bin/windows/contrib/2.4/kidpack_1.4.1.zip mac.binary.ver: bin/macosx/universal/contrib/2.4/kidpack_1.4.1.tgz vignettes: vignettes/kidpack/inst/doc/kidpack.pdf Package: lungExpression Version: 0.0.1 Depends: R (>= 2.4.0), Biobase (>= 1.13.0) Title: Lung cancer gene expression data Description: Data from three large lung cancer studies provided as ExpressionSets biocViews: ExperimentData Author: Robert Scharpf , Simens Zhong , Giovanni Parmigiani Maintainer: Robert Scharpf License: GPL version 2 or newer source.ver: src/contrib/lungExpression_0.0.1.tar.gz Package: lymphoma Version: 1.6.4 Depends: R (>= 2.0.1) Suggests: Biobase, multtest, vsn, marray, limma, arrayMagic Title: Simple exercises on cDNA handling with Alizadeh data Description: Data from 8 chips from Ash Alizadehs Lymphoma paper (Nature 2000); see http://llmpp.nih.gov/lymphoma/ Author: Wolfgang Huber, Andreas Buness, Markus Ruschhaupt, Achim Tresch Maintainer: W. Huber License: LGPL source.ver: src/contrib/lymphoma_1.6.4.tar.gz vignettes: vignettes/lymphoma/inst/doc/candidateGenes.pdf, vignettes/lymphoma/inst/doc/ex.pdf Package: MAQCsubset Version: 1.0.1 Depends: Biobase Title: Experimental Data Package: MAQCsubset Description: Data Package automatically created on Sun Nov 19 15:59:29 2006. biocViews: ExperimentData Author: VJ Carey Maintainer: VJ Carey, License: The Artistic License, Version 2.0 source.ver: src/contrib/MAQCsubset_1.0.1.tar.gz vignettes: vignettes/MAQCsubset/inst/doc/maqcNotes-003.pdf Package: MEEBOdata Version: 1.0.0 Title: MEEBO set and MEEBO controls. Description: R objects describing the MEEBO set. biocViews: ExperimentData Author: Agnes Paquet Maintainer: Agnes Paquet URL: http://alizadehlab.stanford.edu/ http://arrays.ucsf.edu/ License: LGPL source.ver: src/contrib/MEEBOdata_1.0.0.tar.gz win.binary.ver: bin/windows/contrib/2.4/MEEBOdata_1.0.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.4/MEEBOdata_1.0.0.tgz Package: ppiData Version: 0.0.9 Depends: Rgraphviz, graph Suggests: YEAST Title: A package that contains the bait to prey directed graphs for protein-protein interactions. Description: This package contains the directed graphs for protein interaction data as derived from Y2H and APMS as well as the code used to obtain the y2h data from IntAct Repository. Author: Tony Chiang Maintainer: Tony Chiang License: Artistic, Version 2.0 source.ver: src/contrib/ppiData_0.0.9.tar.gz win.binary.ver: bin/windows/contrib/2.4/ppiData_0.0.8.zip vignettes: vignettes/ppiData/inst/doc/ppiStats.pdf Package: ProData Version: 0.4.1 Depends: R (>= 2.4.0), Biobase (>= 1.12.0) Title: SELDI-TOF data of Breast cancer samples Description: A data package of SELDI-TOF protein mass spectrometry data of 167 breast cancer and normal samples. biocViews: ExperimentData Author: Xiaochun Li Maintainer: Xiaochun Li License: GPL source.ver: src/contrib/ProData_0.4.1.tar.gz win.binary.ver: bin/windows/contrib/2.4/ProData_0.4.1.zip mac.binary.ver: bin/macosx/universal/contrib/2.4/ProData_0.4.1.tgz Package: rfcdmin Version: 1.6.0 Depends: R (>= 2.4.0) Title: Minimal Data Library for RFlowCyt examples Description: Provides basic data sets for examples and should be loaded before the package 'rflowcyt' and 'rfcprim'. biocViews: ExperimentData Author: A.J. Rossini, J.Y. Wan, N. Le Meur and Zoe Moodie Maintainer: N. Le Meur URL: http://www.analytics.washington.edu/downloads/rflowcyt/ License: GPL 2.0 source.ver: src/contrib/rfcdmin_1.6.0.tar.gz win.binary.ver: bin/windows/contrib/2.4/rfcdmin_1.6.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.4/rfcdmin_1.6.0.tgz Package: SNAData Version: 1.8.0 Depends: R (>= 2.4.0), graph Suggests: Rgraphviz Title: Social Networks Analysis Data Examples Description: Data from Wasserman & Faust (1999) "Social Network Analysis" biocViews: ExperimentData Author: Denise Scholtens Maintainer: Denise Scholtens License: LGPL source.ver: src/contrib/SNAData_1.8.0.tar.gz win.binary.ver: bin/windows/contrib/2.4/SNAData_1.8.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.4/SNAData_1.8.0.tgz vignettes: vignettes/SNAData/inst/doc/SNAData.pdf Package: SpikeIn Version: 1.4.0 Depends: R (>= 1.6), affy (>= 1.0) Title: Affymetrix Spike-In Experiment Data Description: Contains the HGU133 and HGU95 spikein experiment data. biocViews: ExperimentData Author: Rafael Irizarry Maintainer: Rafael A. Irizarry License: LGPL source.ver: src/contrib/SpikeIn_1.4.0.tar.gz win.binary.ver: bin/windows/contrib/2.4/SpikeIn_1.4.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.4/SpikeIn_1.4.0.tgz Package: SpikeInSubset Version: 1.2.1 Depends: R (>= 2.4.0), Biobase (>= 1.12.0), affy (>= 1.0) Title: Part of Affymetrix's Spike-In Experiment Data Description: Includes probe-level and expression data for the HGU133 and HGU95 spike-in experiments biocViews: ExperimentData Author: Rafael Irizarry and Zhijin Wu Maintainer: Rafael A. Irizarry License: LGPL source.ver: src/contrib/SpikeInSubset_1.2.1.tar.gz win.binary.ver: bin/windows/contrib/2.4/SpikeInSubset_1.2.1.zip mac.binary.ver: bin/macosx/universal/contrib/2.4/SpikeInSubset_1.2.1.tgz Package: stjudem Version: 1.2.0 Depends: R (>= 2.0.0), utils Title: Microarray Data from Yeoh et al. in MACAT format Description: This is a microarray data set on acute lymphoblastic leukemia, published in 2002 (Yeoh et al.Cancer Cell 2002). The experiments were conducted in the St.Jude Children's Research Hospital, Memphis, Tenessee, USA. The raw data was preprocessed by variance stabilizing normalization (Huber et al.) on probe and subsequent summarization of probe expression values into probe set expression values using median polish. biocViews: ExperimentData Author: Benjamin Georgi, Matthias Heinig, Sebastian Schmeier, Joern Toedling Maintainer: Joern Toedling License: LGPL version 2 or above source.ver: src/contrib/stjudem_1.2.0.tar.gz win.binary.ver: bin/windows/contrib/2.4/stjudem_1.2.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.4/stjudem_1.2.0.tgz Package: yeastCC Version: 1.2.2 Depends: Biobase (>= 1.12.0) Title: Spellman et al. (1998) yeast cell cycle microarray data Description: exprSet for Spellman et al. (1998) yeast cell cycle microarray experiment biocViews: ExperimentData Author: Sandrine Dudoit Maintainer: Sandrine Dudoit License: unknown source.ver: src/contrib/yeastCC_1.2.2.tar.gz win.binary.ver: bin/windows/contrib/2.4/yeastCC_1.2.1.zip mac.binary.ver: bin/macosx/universal/contrib/2.4/yeastCC_1.2.1.tgz vignettes: vignettes/yeastCC/inst/doc/Spellmanetal.pdf Package: yeastExpData Version: 0.8.3 Depends: R (>= 2.4), graph (>= 1.9.26) Title: Yeast Experimental Data Description: A collection of different sets of experimental data from yeast. Author: R. Gentleman Maintainer: R. Gentleman License: GPL source.ver: src/contrib/yeastExpData_0.8.3.tar.gz win.binary.ver: bin/windows/contrib/2.4/yeastExpData_0.8.0.zip mac.binary.ver: bin/macosx/universal/contrib/2.4/yeastExpData_0.8.0.tgz vignettes: vignettes/yeastExpData/inst/doc/yeastExample.pdf